The UK-based Syrian Observatory For Human Rights said fighting broke out in three separate locations across the Daraa region at dawn.
If confirmed, the clashes would be among the deadliest attacks by rebel troops since the uprising began nine months ago.
While there was no immediate claim of responsibility, the Free Syrian Army, a Turkish-based defector group, has in the past claimed similar attacks.
The outbreak of violence came as a new report revealed that Syrian troops have been ordered to use "all means necessary" to halt protests, including firing at demonstrators.
Human Rights Watch interviewed dozens of army and intelligence defectors who claimed they were authorised, and in some cases instructed, to use lethal force.
A special forces soldier said he was told to use "as many bullets as you like" against anti-government protesters in Deraa in April. Read More